Here's how to set up FFAStrans 0.7.0 to transcode QuickTime reference files. Attached to this post you will find a package that contains an example workflow and a "Custom AviSynth-script"-preset to make it all happen. This example also demonstrate how the "Custom AviSynth-script"-node can act as a custom decoder: You may add a filter directly after, or a "A/V Media"-decoder for increased decoding reliability, or connect directly to an encoder.

Installation instructions:
1. Make sure you have no less than version 0.7.0 of FFAStrans installed
2. Install the QuickTime package from Apple: http://www.apple.com/quicktime
3. Unpack the attached "QT-ref_example.7z" to your FFAStrans folder. Overwriting does not destroy your installation.
4. Insert your own paths in the "Folder" monitor and delivery node.

Please note that the importand node here is the "Custom AviSynth-script"-node with the "Add support for QT reference"-preset. The rest is just for creating a working example.

As per my understanding QT reference file is reference file to play source file. I am not sure about QTSource function.

If I used above attached example I am getting output as per my encoding setting. I am not able to to play my original hi-res source file using QTReference file.
I have attached media info of source file and QT reference file which I have created using FCP. If you compare both the media info's you will get all the parameters equivalent to each other. Only difference I have observed is file size and one line added in reference file which is source file location. If I play QTReference file created using FCP I am able to play source file.

The QTSource function is needed to read QT reference files. It uses the QuickTime SDK to open the files, that's why you need to install QuickTime from Apple. FFmpeg cannot do this by itself, that's why QT reference files requires special treatment, because they are special.

Now, I'm not sure I quite understand what your post actually is about because the way I understand it, the workflow does what's expected. Is that right? Also, you seem to have a playback problem with our QT reference files?

In the latest 0.9.2 release, the users of the QT reference approach might need to add "color = 0" (RGB24) or "color = 1" (RGB32) to their QTInput string. The latest AviSynth+ release(s) does not deal well with the default YUY2 output coming from the QTSource plugin.
From the example workflow in this thread: